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cailab-tamu / scTenifoldKnk

R/MATLAB package to perform virtual knockout experiments on single-cell gene regulatory networks.
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The dims contain missing values? #21

Open Siteng999 opened 1 year ago

Siteng999 commented 1 year ago

[Dear dosorio

Thank you for your provide convenience.

When I used scTenifoldKnk, the following errors appeared in some experiments, but I checked the matrix and found that there was no missing values. Do you have any solutions?

Warning message: In asMethod(object) : sparse->dense coercion: allocating vector of size 1.4 GiB Error in dim(mat) <- new_modes : the dims contain missing values Calls: scTenifoldKnk ... -> cpDecomposition -> rs_unfold -> unfold In addition: There were 21 warnings (use warnings() to see them) Execution halted

Gratefully， siteng](url)

shelbyhavel commented 1 year ago

I'm also having the same issue, have you found any solutions?

Siteng999 commented 1 year ago

The reason for the above problem is that you don't have enough computing resources. you may consider reducing the number of genes in order to successfully complete the virtual KO. By the way. check if the expression of the candidate genes is strong enough in order to pass the set cut-off threshold.